Locus 283

Sequence ID dm3.chr2L
Location 2,058,222 – 2,058,347
Length 125
Max. P 0.992592
window388 window389 window390

overview

Window 8

Location 2,058,222 – 2,058,312
Length 90
Sequences 7
Columns 117
Reading direction reverse
Mean pairwise identity 69.02
Shannon entropy 0.51643
G+C content 0.56957
Mean single sequence MFE -25.72
Consensus MFE -14.41
Energy contribution -13.64
Covariance contribution -0.77
Combinations/Pair 1.39
Mean z-score -1.74
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.60
SVM RNA-class probability 0.954234
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2058222 90 - 23011544
------------AAACAGCUCGGCAGACCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGC--CGUGGAGCAAC-CCCAUCCA-GUGGC--UCCCAUCCCCC---------
------------........((((((((.....(((((((.........)))))))...))))..))--)).(((((.((-........-)).))--)))........--------- ( -26.00, z-score =  -2.13, R)
>droSim1.chr2L 2028471 90 - 22036055
------------AAACAGCUCGGCAGACCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGC--CGUGGAGCAAC-CCCAUCCA-GUGGC--CCCCAUCCCCC---------
------------.........((.((((.....(((((((.........)))))))...))))))((--((((((.....-....))))-.))))--...........--------- ( -24.20, z-score =  -1.55, R)
>droSec1.super_14 2005010 90 - 2068291
------------AAACAGCUCGGCAGACCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGC--CGUGGAGCAAC-CCCAUCCA-GUGGC--CCCCAUCCCUC---------
------------.........((.((((.....(((((((.........)))))))...))))))((--((((((.....-....))))-.))))--...........--------- ( -24.20, z-score =  -1.47, R)
>droYak2.chr2L 2044302 92 - 22324452
------------ACACAGCUUGGCAGACCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGC--CGUGGAGCAAC-CCCAUCCA-GUGUCCAUCCCAUUCCCA---------
------------((((.....(((((((.....(((((((.........)))))))...))))..))--).((((.....-....))))-))))..............--------- ( -22.50, z-score =  -1.36, R)
>droEre2.scaffold_4929 2106382 98 - 26641161
------------AAACA-CUCGGCAGACCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGC--CGUGGAGCAAC-CCCAUCCA-GUGGC--ACCCAGCCGCACCAUCCCCA
------------.....-..((((((((.....(((((((.........)))))))...))))..))--))((((.....-....))))-(((((--.....))))).......... ( -28.90, z-score =  -2.43, R)
>dp4.chr4_group3 8856264 117 - 11692001
AAAACAACGCGGCAAAAGUUCAGCGUGCCGCAAGAUGGUGCCAUAAAAACGCCAUUACUGUCCCUACCACACACACAGAUACGCAUACACAUACACAGAGGACCUGCACCGUCACCA
........((((((...(.....).))))))..((((((((.........((.....((((.............))))....))............((.....)))))))))).... ( -27.02, z-score =  -1.56, R)
>droPer1.super_8 38474 115 - 3966273
AAAACAACGCGGCAAAAGUUCAGCGUGCCGCAAGAUGGUGCCAUAAAAACGCCAUUACUGUCCCUAC--CACACACAGAUACGCAUACACAUACACAGAGGACCUGCACCGUCACCA
........((((((...(.....).))))))..((((((((.........((.....((((......--.....))))....))............((.....)))))))))).... ( -27.20, z-score =  -1.66, R)
>consensus
____________AAACAGCUCGGCAGACCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGC__CGUGGAGCAAC_CCCAUCCA_GUGGC__CCCCAUCCCCA_________
....................(((.((((.....(((((((.........)))))))...)))))))....((((........))))............................... (-14.41 = -13.64 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,058,251 – 2,058,347
Length 96
Sequences 8
Columns 120
Reading direction forward
Mean pairwise identity 68.74
Shannon entropy 0.55554
G+C content 0.46801
Mean single sequence MFE -31.01
Consensus MFE -14.34
Energy contribution -14.38
Covariance contribution 0.03
Combinations/Pair 1.31
Mean z-score -2.50
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.55
SVM RNA-class probability 0.992592
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2058251 96 + 23011544
-------UCCACGGCGGAGACAGUAAUGGCGUUUUUACGGCGCCAUCUUGAGG-----------UCUGCCGAGCUGUUU-GUUGUUACAACAUUUGCGUUAUUCUUUUUUCGGAC-----
-------(((.(((((((....(..((((((((.....))))))))..)....-----------))))))).((....(-((((...)))))...))..............))).----- ( -30.60, z-score =  -2.13, R)
>droSim1.chr2L 2028500 96 + 22036055
-------UCCACGGCGGAGACAGUAAUGGCGUUUUUACGGCGCCAUCUUGAGG-----------UCUGCCGAGCUGUUU-GUUGUAACAACAUUUGCGUUAUUCUUUCCUCCGCC-----
-------.....((((((((((((.((((((((.....)))))))).....((-----------....))..))))).(-((((...)))))................)))))))----- ( -32.20, z-score =  -2.28, R)
>droSec1.super_14 2005039 84 + 2068291
-------UCCACGGCGGAGACAGUAAUGGCGUUUUUACGGCGCCAUCUUGAGG-----------UCUGCCGAGCUGUUU-GUUGUAACAACAUUUGC-UCCGCC----------------
-------.....((((((((((((.((((((((.....)))))))).....((-----------....))..))))).(-((((...)))))....)-))))))---------------- ( -32.10, z-score =  -2.71, R)
>droYak2.chr2L 2044333 96 + 22324452
-------UCCACGGCGGAGACAGUAAUGGCGUUUUUACGGCGCCAUCUUGAGG-----------UCUGCCAAGCUGUGU-GUUGUAACAACGAUUUCGUUAUUCUUUUCGCCGCC-----
-------....(((((((((.((((((((((((.(((((((((((.((((...-----------.....)))).)).))-))))))).))))...)))))))).)))))))))..----- ( -38.20, z-score =  -3.86, R)
>droEre2.scaffold_4929 2106420 100 + 26641161
-------UCCACGGCGGAGACAGUAAUGGCGUUUUUACGGCGCCAUCUUGAGG-----------UCUGCCGAGUGUUU--GUCGUAACAACAUUUUCGUUAUUCUUUUCUCCGCCACAAC
-------.....((((((((.((.(((((((......(((((((.......))-----------)..))))((((((.--((....))))))))..))))))).)).))))))))..... ( -34.10, z-score =  -3.32, R)
>droAna3.scaffold_12916 9773194 75 - 16180835
---------UCUGGUGGAGACAGUAAUGGCGUUUUUAUGGCGCCAUCUUGAGG-----------UCU---------CU--GGUAUAAUAAUAUUUUUGUUUUAUUU--------------
---------......((((((.(..((((((((.....))))))))..)...)-----------)))---------))--((((.(((((.....))))).)))).-------------- ( -20.90, z-score =  -3.00, R)
>dp4.chr4_group3 8856301 114 + 11692001
AUCUGUGUGUGUGGUAGGGACAGUAAUGGCGUUUUUAUGGCACCAUCUUGCGGCACGCUGAACUUUUGCCGCGUUGUUUUGUUGUAAUAAUAUUUUCCUCUGCCGUUUCUUUUU------
............((((((((((....))..(((.(((..(((..((..(((((((...........)))))))..))..)))..))).)))....))).)))))..........------ ( -30.00, z-score =  -1.22, R)
>droPer1.super_8 38511 112 + 3966273
--AUCUGUGUGUGGUAGGGACAGUAAUGGCGUUUUUAUGGCACCAUCUUGCGGCACGCUGAACUUUUGCCGCGUUGUUUUGUUGUAAUAAUAUUUUCCUCUGCCGUUUCUUUUU------
--..........((((((((((....))..(((.(((..(((..((..(((((((...........)))))))..))..)))..))).)))....))).)))))..........------ ( -30.00, z-score =  -1.45, R)
>consensus
_______UCCACGGCGGAGACAGUAAUGGCGUUUUUACGGCGCCAUCUUGAGG___________UCUGCCGAGCUGUUU_GUUGUAACAACAUUUUCGUUAUUCUUUUCUCCGC______
...........(((((((.......((((((((.....))))))))(....)............)))))))................................................. (-14.34 = -14.38 +   0.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,058,251 – 2,058,347
Length 96
Sequences 8
Columns 120
Reading direction reverse
Mean pairwise identity 68.74
Shannon entropy 0.55554
G+C content 0.46801
Mean single sequence MFE -26.98
Consensus MFE -8.96
Energy contribution -9.40
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -2.54
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.34
SVM RNA-class probability 0.928753
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2058251 96 - 23011544
-----GUCCGAAAAAAGAAUAACGCAAAUGUUGUAACAAC-AAACAGCUCGGCAGA-----------CCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGCCGUGGA-------
-----.((((...................(((((......-..))))).(((((((-----------(.....(((((((.........)))))))...))))..))))))))------- ( -23.70, z-score =  -1.30, R)
>droSim1.chr2L 2028500 96 - 22036055
-----GGCGGAGGAAAGAAUAACGCAAAUGUUGUUACAAC-AAACAGCUCGGCAGA-----------CCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGCCGUGGA-------
-----((((((((..((......((....((((((.....-.))))))...))...-----------......(((((((.........))))))).)).)))))))).....------- ( -32.70, z-score =  -2.65, R)
>droSec1.super_14 2005039 84 - 2068291
----------------GGCGGA-GCAAAUGUUGUUACAAC-AAACAGCUCGGCAGA-----------CCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGCCGUGGA-------
----------------((((((-((....((((((.....-.))))))...)).((-----------(.....(((((((.........)))))))...))))))))).....------- ( -30.40, z-score =  -2.57, R)
>droYak2.chr2L 2044333 96 - 22324452
-----GGCGGCGAAAAGAAUAACGAAAUCGUUGUUACAAC-ACACAGCUUGGCAGA-----------CCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGCCGUGGA-------
-----.(((((......(((((((....))))))).....-.........((.(((-----------(.....(((((((.........)))))))...)))))))))))...------- ( -30.10, z-score =  -1.89, R)
>droEre2.scaffold_4929 2106420 100 - 26641161
GUUGUGGCGGAGAAAAGAAUAACGAAAAUGUUGUUACGAC--AAACACUCGGCAGA-----------CCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGCCGUGGA-------
.(..(((((((((..((.....(((.....((((....))--))....))).....-----------......(((((((.........))))))).)).)))))))))..).------- ( -31.90, z-score =  -2.30, R)
>droAna3.scaffold_12916 9773194 75 + 16180835
--------------AAAUAAAACAAAAAUAUUAUUAUACC--AG---------AGA-----------CCUCAAGAUGGCGCCAUAAAAACGCCAUUACUGUCUCCACCAGA---------
--------------..........................--.(---------(((-----------(.....(((((((.........)))))))...))))).......--------- ( -14.40, z-score =  -4.32, R)
>dp4.chr4_group3 8856301 114 - 11692001
------AAAAAGAAACGGCAGAGGAAAAUAUUAUUACAACAAAACAACGCGGCAAAAGUUCAGCGUGCCGCAAGAUGGUGCCAUAAAAACGCCAUUACUGUCCCUACCACACACACAGAU
------..........((.((.(((.......................((((((...(.....).))))))..(((((((.........)))))))....))))).))............ ( -26.30, z-score =  -2.64, R)
>droPer1.super_8 38511 112 - 3966273
------AAAAAGAAACGGCAGAGGAAAAUAUUAUUACAACAAAACAACGCGGCAAAAGUUCAGCGUGCCGCAAGAUGGUGCCAUAAAAACGCCAUUACUGUCCCUACCACACACAGAU--
------..........((.((.(((.......................((((((...(.....).))))))..(((((((.........)))))))....))))).))..........-- ( -26.30, z-score =  -2.62, R)
>consensus
______GCGGAGAAAAGAAUAACGAAAAUGUUGUUACAAC_AAACAGCUCGGCAGA___________CCUCAAGAUGGCGCCGUAAAAACGCCAUUACUGUCUCCGCCGUGGA_______
..................................................(((((.............(....)((((((.........))))))..))))).................. ( -8.96 =  -9.40 +   0.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:10:04 2011